BHC 1.25.0
Rich Savage
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BHC | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BHC_1.25.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/BHC.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BHC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BHC’ version ‘1.25.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BHC’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
FindOptimalHyperparameter: no visible global function definition for
‘optimise’
WriteOutClusterLabels : WhereToCut: no visible global function
definition for ‘is.leaf’
WriteOutClusterLabels: no visible global function definition for
‘dendrapply’
WriteOutClusterLabels: no visible global function definition for
‘write.table’
Undefined global functions or variables:
dendrapply is.leaf optimise write.table
Consider adding
importFrom("stats", "dendrapply", "is.leaf", "optimise")
importFrom("utils", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work. If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘BHC/libs/BHC.so’:
Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
Objects: ‘BlockCovarianceMatrix.o’,
‘CubicSplineTimecourseDataSet.o’, ‘DataSet.o’,
‘DirichletProcessMixture.o’, ‘MultinomialDataSet.o’, ‘Node.o’,
‘RobustCubicSplineTimecourseDataSet.o’,
‘SquaredExponentialTimecourseDataSet.o’, ‘TimecourseDataSet.o’,
‘bhc.o’, ‘multinomial_OutputDendrogramInformation.o’,
‘multinomial_ReadInData.o’
Found ‘_srand’, possibly from ‘srand’ (C)
Object: ‘DirichletProcessMixture.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.4-bioc/meat/BHC.Rcheck/00check.log’
for details.
* installing *source* package ‘BHC’ ...
checking for gcc... clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking for clang option to support OpenMP... unsupported
configure: WARNING: No OpenMP support. If using GCC, upgrade to >= 4.2
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c BlockCovarianceMatrix.cpp -o BlockCovarianceMatrix.o
In file included from BlockCovarianceMatrix.cpp:15:
In file included from ./BlockCovarianceMatrix.h:16:
./header.h:16:9: warning: 'NDEBUG' macro redefined
#define NDEBUG
^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c CubicSplineTimecourseDataSet.cpp -o CubicSplineTimecourseDataSet.o
In file included from CubicSplineTimecourseDataSet.cpp:15:
In file included from ./CubicSplineTimecourseDataSet.h:20:
In file included from ./TimecourseDataSet.h:20:
In file included from ./DataSet.h:16:
./header.h:16:9: warning: 'NDEBUG' macro redefined
#define NDEBUG
^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
^
In file included from CubicSplineTimecourseDataSet.cpp:15:
./CubicSplineTimecourseDataSet.h:29:10: warning: 'CubicSplineTimecourseDataSet::GetMLIINoise' hides overloaded virtual function [-Woverloaded-virtual]
double GetMLIINoise(const vector<int>& itemIndex);
^
./TimecourseDataSet.h:36:10: note: hidden overloaded virtual function 'TimecourseDataSet::GetMLIINoise' declared here: type mismatch at 1st parameter ('vector<int>' vs 'const vector<int> &')
double GetMLIINoise(vector<int> itemIndex);
^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c DataSet.cpp -o DataSet.o
In file included from DataSet.cpp:13:
In file included from ./DataSet.h:16:
./header.h:16:9: warning: 'NDEBUG' macro redefined
#define NDEBUG
^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
^
DataSet.cpp:36:48: warning: if statement has empty body [-Wempty-body]
if(!system("PAUSE")) /* could not pause */ ;
^
DataSet.cpp:36:48: note: put the semicolon on a separate line to silence this warning
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c DirichletProcessMixture.cpp -o DirichletProcessMixture.o
In file included from DirichletProcessMixture.cpp:15:
In file included from ./DirichletProcessMixture.h:4:
./header.h:16:9: warning: 'NDEBUG' macro redefined
#define NDEBUG
^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c MultinomialDataSet.cpp -o MultinomialDataSet.o
In file included from MultinomialDataSet.cpp:1:
In file included from ./MultinomialDataSet.h:4:
In file included from ./DataSet.h:16:
./header.h:16:9: warning: 'NDEBUG' macro redefined
#define NDEBUG
^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
^
In file included from MultinomialDataSet.cpp:1:
./MultinomialDataSet.h:19:10: warning: 'MultinomialDataSet::SingleClusterLogEvidence' hides overloaded virtual function [-Woverloaded-virtual]
double SingleClusterLogEvidence(vector<int> itemIndex); // returns the log-evidence for a cluster that contains data items defined by itemIndex
^
./DataSet.h:29:18: note: hidden overloaded virtual function 'DataSet::SingleClusterLogEvidence' declared here: different number of parameters (5 vs 1)
virtual double SingleClusterLogEvidence(const vector<int>& itemIndex,
^
MultinomialDataSet.cpp:77:43: warning: if statement has empty body [-Wempty-body]
if(!system("PAUSE"))/* didn't pause */;
^
MultinomialDataSet.cpp:77:43: note: put the semicolon on a separate line to silence this warning
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c Node.cpp -o Node.o
In file included from Node.cpp:13:
In file included from ./Node.h:16:
./header.h:16:9: warning: 'NDEBUG' macro redefined
#define NDEBUG
^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c RobustCubicSplineTimecourseDataSet.cpp -o RobustCubicSplineTimecourseDataSet.o
In file included from RobustCubicSplineTimecourseDataSet.cpp:15:
In file included from ./RobustCubicSplineTimecourseDataSet.h:20:
In file included from ./CubicSplineTimecourseDataSet.h:20:
In file included from ./TimecourseDataSet.h:20:
In file included from ./DataSet.h:16:
./header.h:16:9: warning: 'NDEBUG' macro redefined
#define NDEBUG
^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
^
In file included from RobustCubicSplineTimecourseDataSet.cpp:15:
In file included from ./RobustCubicSplineTimecourseDataSet.h:20:
./CubicSplineTimecourseDataSet.h:29:10: warning: 'CubicSplineTimecourseDataSet::GetMLIINoise' hides overloaded virtual function [-Woverloaded-virtual]
double GetMLIINoise(const vector<int>& itemIndex);
^
./TimecourseDataSet.h:36:10: note: hidden overloaded virtual function 'TimecourseDataSet::GetMLIINoise' declared here: type mismatch at 1st parameter ('vector<int>' vs 'const vector<int> &')
double GetMLIINoise(vector<int> itemIndex);
^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c RobustSquaredExponentialTimecourseDataSet.cpp -o RobustSquaredExponentialTimecourseDataSet.o
In file included from RobustSquaredExponentialTimecourseDataSet.cpp:15:
In file included from ./RobustSquaredExponentialTimecourseDataSet.h:20:
In file included from ./SquaredExponentialTimecourseDataSet.h:20:
./header.h:16:9: warning: 'NDEBUG' macro redefined
#define NDEBUG
^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c SquaredExponentialTimecourseDataSet.cpp -o SquaredExponentialTimecourseDataSet.o
In file included from SquaredExponentialTimecourseDataSet.cpp:15:
In file included from ./SquaredExponentialTimecourseDataSet.h:20:
./header.h:16:9: warning: 'NDEBUG' macro redefined
#define NDEBUG
^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c TimecourseDataSet.cpp -o TimecourseDataSet.o
In file included from TimecourseDataSet.cpp:13:
In file included from ./TimecourseDataSet.h:20:
In file included from ./DataSet.h:16:
./header.h:16:9: warning: 'NDEBUG' macro redefined
#define NDEBUG
^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
^
TimecourseDataSet.cpp:80:40: warning: if statement has empty body [-Wempty-body]
if(!system("PAUSE"))/*didn't work*/;
^
TimecourseDataSet.cpp:80:40: note: put the semicolon on a separate line to silence this warning
TimecourseDataSet.cpp:143:40: warning: if statement has empty body [-Wempty-body]
if(!system("PAUSE"))/*didn't work*/;
^
TimecourseDataSet.cpp:143:40: note: put the semicolon on a separate line to silence this warning
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c bhc.cpp -o bhc.o
In file included from bhc.cpp:17:
./header.h:16:9: warning: 'NDEBUG' macro redefined
#define NDEBUG
^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
^
In file included from bhc.cpp:20:
./CubicSplineTimecourseDataSet.h:29:10: warning: 'CubicSplineTimecourseDataSet::GetMLIINoise' hides overloaded virtual function [-Woverloaded-virtual]
double GetMLIINoise(const vector<int>& itemIndex);
^
./TimecourseDataSet.h:36:10: note: hidden overloaded virtual function 'TimecourseDataSet::GetMLIINoise' declared here: type mismatch at 1st parameter ('vector<int>' vs 'const vector<int> &')
double GetMLIINoise(vector<int> itemIndex);
^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c gammaln.cpp -o gammaln.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c header.cpp -o header.o
In file included from header.cpp:1:
./header.h:16:9: warning: 'NDEBUG' macro redefined
#define NDEBUG
^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c multinomial_CalculateHyperparameters.cpp -o multinomial_CalculateHyperparameters.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c multinomial_OutputDendrogramInformation.cpp -o multinomial_OutputDendrogramInformation.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c multinomial_ReadInData.cpp -o multinomial_ReadInData.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c multinomial_bayeslink_binf.cpp -o multinomial_bayeslink_binf.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c multinomial_binevidence.cpp -o multinomial_binevidence.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o BHC.so BlockCovarianceMatrix.o CubicSplineTimecourseDataSet.o DataSet.o DirichletProcessMixture.o MultinomialDataSet.o Node.o RobustCubicSplineTimecourseDataSet.o RobustSquaredExponentialTimecourseDataSet.o SquaredExponentialTimecourseDataSet.o TimecourseDataSet.o bhc.o gammaln.o header.o multinomial_CalculateHyperparameters.o multinomial_OutputDendrogramInformation.o multinomial_ReadInData.o multinomial_bayeslink_binf.o multinomial_binevidence.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/BHC.Rcheck/BHC/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BHC)